Help installing software into Linux (Ubuntu)

Discussion in 'Tech Talk' started by GixxerSixxer, Aug 23, 2007.

  1. GixxerSixxer

    GixxerSixxer Phil Deez Nutz

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    I need to install some software that allows me to view protein structures for a class I'm taking.

    I can't get through the install process and need some help.

    Here is the site: http://delsci.com/rel/099/

    Here are the instructions:

    Step 1 is easy and taken care of.

    At Step 2 I open the terminal and paste the supplied command and get an error.

    I changed the tar -zxf pymol-0_99rc1-bin-linux-x86-glibc23.tgz
    to tar -zxf pymol-0_99rc6 -bin-linux-x86-glibc23.tgz but I still get an error.

    What am I doing wrong?

    Thanks
     
  2. Washington D.C.

    Washington D.C.

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    http://www.pymolwiki.org/index.php/Linux_Install


    Ubuntu Linux (x86 32,64; mac ppc)

    http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

    The Ubuntu pymol package can be installed with minimal effort using the GUI package manager synaptic, or on the command line, using the command

    sudo apt-get install pymol

    once the universe repository has been activated.

    Ubuntu is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using Ubuntu for crystallography and related applications are available are linked. PyMol also compiles from source on Ubuntu following the #Generic Linux instructions given above.
     

  3. Washington D.C.

    Washington D.C.

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  4. Washington D.C.

    Washington D.C.

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  5. IndyGunFreak

    IndyGunFreak

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    1st... Pymol is in the repositories(just noticed DC mentioned that). Install it from there.

    Second, it'd be REALLY helpful to know the error your getting. Are you getting the "Unterminated String" error? I didn't mess with it to much but following their instructions definitely doesn't work. I suspect its an error with the installer.

    FWIW though, I just installed the version from the repos on my laptop, and it worked fine. Once you install the version from the repos, it will be in the Applications/Education menu, and although I have no clue what it does, :), it seems to work fine.

    IGF
     
  6. Washington D.C.

    Washington D.C.

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    For PyMol to work properly you need 3d video drivers installed. "OpenGL drivers."


    On Linux, you need the following requirements:

    * Python (with distutils)
    * Pmw (Python Megawidgets)
    * OpenGL driver
     
  7. GixxerSixxer

    GixxerSixxer Phil Deez Nutz

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    Thanks for all the help!

    I didn't think Pymol was big enough to make it into the repositories, that should make things easier.

    And to finalize things I should get:

    * Python (with distutils)
    * Pmw (Python Megawidgets)
    * OpenGL driver

    from the repositories as well to run things right?

    I have universe and multiverse enabled already from when I getting the WMV Codecs.
     
  8. Washington D.C.

    Washington D.C.

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    What hardware are you using? Do you know your video card? Which version of Ubuntu are you using?
     
  9. GixxerSixxer

    GixxerSixxer Phil Deez Nutz

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    I have a 512, 60GB Dell 600m.

    I don't know the video card. I've tried to see if Ubuntu can tell me what it is but can't find it.

    I'm running "Edgy".
     
  10. Washington D.C.

    Washington D.C.

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    Okay I haven't run Ubuntu in a while but I think Edgy is 6.10. I'm not sure about how current the open source video drivers are in it. Recently the Intel graphics got 3d working in Linux. ATI is not as difficult as it used to be but still might be trouble as might Intel with older versions of Linux. Ubuntu is up to 7.04 now. With Nvidia video you must download the drivers from the Nvidia website. There may be something in Edgy to tell you or watch the screen at boot and see if it says. Maybe check the Dell website and enter the serial number of the PC. That should work. You will need to know to get OpenGL working(3d).
     
  11. Washington D.C.

    Washington D.C.

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    It looks like the Dell Inspiron 600M might have ATI Mobility Radeon 9000 graphics.
     
  12. Washington D.C.

    Washington D.C.

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  13. Washington D.C.

    Washington D.C.

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    Some more instructions. You won't need Beryl and XGL. These are just for 3d desktop not 3d graphics that you require but has good ATI FGLRX driver install info.

    http://ubuntuforums.org/showthread.php?t=291464

    With 512MB of RAM I wouldn't try running Beryl/XDL but the ATI FGLRX 3d drivers should be fine but Beryl takes up some system resouces.
     
  14. Mug

    Mug

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    Well it looks like you have it narrowed down to an ATI card but, for future refernce in determining what hardware you have you can run the command "lspci" which will show you all the hardware info.